diffpy.srreal 1.5.0__cp314-cp314-win_amd64.whl

diffpy/__init__.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2026 diffpy.srreal contributors.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srreal/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################

diffpy/srreal/__init__.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2026 diffpy.srreal contributors.
+# All rights reserved.
+#
+# File coded by: Simon Billinge, Billinge Group members.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srreal/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Calculators for PDF, bond valence sum, and other quantities based on
+atom pair interaction."""
+
+
+# start delvewheel patch
+def _delvewheel_patch_1_13_2():
+    import os
+    if os.path.isdir(libs_dir := os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'diffpy_srreal.libs'))):
+        os.add_dll_directory(libs_dir)
+
+
+_delvewheel_patch_1_13_2()
+del _delvewheel_patch_1_13_2
+# end delvewheel patch
+
+# package version
+from diffpy.srreal.version import __version__  # noqa
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file

diffpy/srreal/_cleanup.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     Complex Modeling Initiative
+#                   (c) 2016 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+"""Cancel registration of Python-extended C++ classes when Python exits.
+
+Note
+----
+Python finishes before the shared library libdiffpy, but the registry of
+class prototypes is implemented in libdiffpy.  Any Python-extended classes
+thus need to be removed from the registry prior to Python exit.
+
+This module is not intended for direct use.  It is used implicitly within
+a call of _registerThisType.
+"""
+
+import atexit
+import weakref
+
+# Routine to be used from srreal_ext module ----------------------------------
+
+
+def registerForCleanUp(obj):
+    """Remember to clean up the specified prototype at Python exit.
+
+    Parameters
+    ----------
+    obj : wrapped class that has class registry
+        This is an object being added to the C++ registry of prototypes.
+        If active at Python exit, the associated string type will be
+        removed from the class registry.
+
+    No return value.
+    """
+    _cleanup_handler.add(obj)
+    return
+
+
+# ----------------------------------------------------------------------------
+
+
+class _DerivedClassesCleanUpHandler(object):
+
+    def __init__(self):
+        self._references = set()
+        return
+
+    def add(self, obj):
+        wr = weakref.ref(obj)
+        self._references.add(wr)
+        return
+
+    def clean(self):
+        while self._references:
+            wr = self._references.pop()
+            obj = wr()
+            if obj is not None:
+                obj._deregisterType(obj.type())
+        return
+
+
+# end of class _DerivedClassesCleanUpHandler
+
+
+# create singleton instance of the cleanup handler
+_cleanup_handler = _DerivedClassesCleanUpHandler()
+atexit.register(_cleanup_handler.clean)
+
+del _DerivedClassesCleanUpHandler
+
+# End of file.

diffpy/srreal/_docstrings.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     Complex Modeling Initiative
+#                   (c) 2016 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+"""Docstrings for classes and functions in srreal_ext module."""
+
+# Shared docstrings for classes derived from HasClassRegistry ----------------
+
+
+def get_registry_docstrings(cls):
+    """Build a dictionary of docstrings per each HasClassRegistry
+    method.
+
+    Parameters
+    ----------
+    cls : class type that is wrapped
+        This parameter is used to extract the class name and substitute
+        it in the docstrings template.
+
+    Returns a dictionary mapping Python method names to their docstrins.
+    """
+    n = cls.__name__
+    rv = {
+        k: v.replace("@NAME@", n)
+        for k, v in (
+            ("create", doc_HasClassRegistry_create),
+            ("clone", doc_HasClassRegistry_clone),
+            ("type", doc_HasClassRegistry_type),
+            ("_registerThisType", doc_HasClassRegistry__registerThisType),
+            ("_aliasType", doc_HasClassRegistry__aliasType),
+            ("_deregisterType", doc_HasClassRegistry__deregisterType),
+            ("createByType", doc_HasClassRegistry_createByType),
+            ("isRegisteredType", doc_HasClassRegistry_isRegisteredType),
+            ("getAliasedTypes", doc_HasClassRegistry_getAliasedTypes),
+            ("getRegisteredTypes", doc_HasClassRegistry_getRegisteredTypes),
+        )
+    }
+    return rv
+
+
+doc_HasClassRegistry_create = """\
+Return a new instance of the same type as self.
+
+This method must be overloaded in a derived class.
+"""
+
+
+doc_HasClassRegistry_clone = """\
+Return a new instance that is a copy of self.
+
+This method must be overloaded in a derived class.
+"""
+
+
+doc_HasClassRegistry_type = """\
+Return a unique string type that identifies a @NAME@-derived class.
+The string type is used for class registration and in the `createByType`
+function.
+
+This method must be overloaded in a derived class.
+"""
+
+
+doc_HasClassRegistry__registerThisType = """\
+Add this class to the global registry of @NAME@ types.
+
+This method must be called once after definition of the derived
+class to support pickling and the `createByType` factory.
+"""
+
+
+doc_HasClassRegistry__aliasType = """\
+Register the specified class type under another string alias.
+
+Parameters
+----------
+tp : str
+    string type identifying a registered @NAME@ class.
+alias : str
+    string alias to be used for the `tp` type.
+
+Raises
+------
+RuntimeError
+    When they `tp` type is unknown or if the `alias` type is already
+    registered.
+"""
+
+
+doc_HasClassRegistry__deregisterType = """\
+Cancel registration of the specified string type and any of its aliases.
+
+Parameters
+----------
+tp : str
+    string type or an alias of a registered @NAME@ class.
+
+Returns
+-------
+count : int
+    Number of unregistered names or aliases.
+    Return 0 if `tp` is not a registered type.
+"""
+
+
+doc_HasClassRegistry_createByType = """\
+Return a new @NAME@ instance of the specified string type.
+
+Parameters
+----------
+tp : str
+    string type identifying a registered @NAME@ class.
+
+Returns
+-------
+@NAME@
+    A new instance of the @NAME@-derived class named `tp`.
+
+See Also
+--------
+getRegisteredTypes : Return set of the recognized type strings.
+getAliasedTypes : Return dictionary of string aliases.
+"""
+
+
+doc_HasClassRegistry_isRegisteredType = """\
+Check if the given string is registered as a named @NAME@ type.
+
+Parameters
+----------
+tp : str
+    string name or an alias to be checked.
+
+Returns
+-------
+bool
+    ``True`` if `tp` is known to the registry either as a standard
+    type or its alias.
+"""
+
+
+doc_HasClassRegistry_getAliasedTypes = """\
+Get all aliases registered for the @NAME@ string types.
+
+Returns
+-------
+dict
+    a map of registered aliases to their corresponding standard names.
+"""
+
+
+doc_HasClassRegistry_getRegisteredTypes = """\
+Get string types of all registered @NAME@ classes.
+
+These are the allowed arguments for the `createByType` factory.
+
+Returns
+-------
+set
+    the registered string types.
+"""

diffpy/srreal/_final_imports.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     Complex Modeling Initiative
+#                   (c) 2016 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+"""Finalize tweak of classes from the extension module srreal_ext.
+
+This private module handles loading of Python-level tweaks of the
+extension-defined classes.  Any client that imports this module must
+call the `import_now` function.  If this module is not loaded by the
+time of srreal_ext initialization, `import_now` is executed from
+srreal_ext.
+
+This avoids unresolvable import dependencies for any order of imports.
+"""
+
+_import_now_called = False
+
+
+def import_now():
+    """Import all Python modules that tweak extension-defined
+    classes."""
+    global _import_now_called
+    if _import_now_called:
+        return
+    _import_now_called = True
+    from importlib import import_module
+
+    import_module("diffpy.srreal.attributes")
+    import_module("diffpy.srreal.atomradiitable")
+    import_module("diffpy.srreal.bondcalculator")
+    import_module("diffpy.srreal.bvscalculator")
+    import_module("diffpy.srreal.overlapcalculator")
+    import_module("diffpy.srreal.pdfbaseline")
+    import_module("diffpy.srreal.pdfenvelope")
+    import_module("diffpy.srreal.peakprofile")
+    import_module("diffpy.srreal.peakwidthmodel")
+    import_module("diffpy.srreal.scatteringfactortable")
+    import_module("diffpy.srreal.pdfcalculator")
+    import_module("diffpy.srreal.structureconverters")
+    return

diffpy/srreal/_objcrystconverters.py

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+"""Copy ObjCryst structures without crossing a C++ library ABI boundary.
+
+Use only pyobjcryst's Python API so both its Boost.Python releases and
+its nanobind migration (with a private, static ObjCryst++ library) can
+be used. Keep the numerical conventions of libdiffpy's
+ObjCrystStructureAdapter.
+"""
+
+import numpy as np
+
+from diffpy.srreal.srreal_ext import (
+    Atom,
+    AtomicStructureAdapter,
+    CrystalStructureAdapter,
+)
+
+
+def _check_type(obj, name):
+    # Import lazily: pyobjcryst is an optional runtime dependency.
+    from pyobjcryst import _pyobjcryst
+
+    if not isinstance(obj, getattr(_pyobjcryst, name)):
+        raise TypeError(f"Expected a pyobjcryst {name} object.")
+
+
+def _atom_from_scattering_power(sp):
+    atom = Atom()
+    atom.atomtype = sp.GetSymbol()
+    atom.anisotropy = not sp.IsIsotropic()
+    if atom.anisotropy:
+        bij = np.array(
+            [[sp.GetBij(i, j) for j in range(1, 4)] for i in range(1, 4)]
+        )
+    else:
+        bij = np.eye(3) * sp.GetBiso()
+    atom.uij_cartn = bij / (8 * np.pi**2)
+    return atom
+
+
+def convertObjCrystMolecule(molecule):
+    """Copy molecule atoms in local Cartesian coordinates, omitting
+    dummies."""
+    _check_type(molecule, "Molecule")
+    adapter = AtomicStructureAdapter()
+    adapter.reserve(molecule.GetNbComponent())
+    for i in range(molecule.GetNbComponent()):
+        source = molecule.GetAtom(i)
+        if source.IsDummy():
+            continue
+        atom = _atom_from_scattering_power(source.GetScatteringPower())
+        atom.xyz_cartn = [source.X, source.Y, source.Z]
+        atom.occupancy = source.Occupancy
+        adapter.append(atom)
+    return adapter
+
+
+def convertObjCrystCrystal(crystal):
+    """Copy the asymmetric unit and complete space-group symmetry
+    operations."""
+    _check_type(crystal, "Crystal")
+    adapter = CrystalStructureAdapter()
+    lattice = [crystal.GetLatticePar(i) for i in range(6)]
+    lattice[3:] = np.degrees(lattice[3:])
+    adapter.setLatPar(*lattice)
+    components = crystal.GetScatteringComponentList()
+    adapter.reserve(len(components))
+    for source in components:
+        sp = source.mpScattPow
+        if sp is None:
+            continue
+        atom = _atom_from_scattering_power(sp)
+        atom.xyz_cartn = [source.mX, source.mY, source.mZ]
+        atom.occupancy = source.mOccupancy
+        # Isotropic U is already Cartesian. Only anisotropic U follows the
+        # lattice transformation; coordinates always need that transformation.
+        uij = atom.uij_cartn.copy()
+        adapter.toCartesian(atom)
+        if not atom.anisotropy:
+            atom.uij_cartn = uij
+        adapter.append(atom)
+
+    sg = crystal.GetSpaceGroup()
+    operations = [
+        (np.asarray(rotation), np.asarray(translation) + offset)
+        for offset in sg.GetTranslationVectors()
+        for translation, rotation in sg.GetSymmetryOperations()
+    ]
+    if len(operations) < sg.GetNbSymmetrics():
+        inversion = 2 * np.asarray(sg.GetInversionCenter())
+        operations += [(-r, inversion - t) for r, t in operations]
+    if len(operations) != sg.GetNbSymmetrics():
+        raise ValueError("Inconsistent pyobjcryst space-group operations.")
+    for rotation, translation in operations:
+        adapter.addSymOp(rotation, translation)
+    adapter.updateSymmetryPositions()
+    return adapter

diffpy/srreal/atomradiitable.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2011 The Trustees of Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+"""Class AtomRadiiTable -- storage of empirical atom radii."""
+
+# exported items, these also makes them show in pydoc.
+__all__ = ["AtomRadiiTable", "ConstantRadiiTable", "CovalentRadiiTable"]
+
+from diffpy.srreal.srreal_ext import AtomRadiiTable, ConstantRadiiTable
+
+# class CovalentRadiiTable ---------------------------------------------------
+
+
+class CovalentRadiiTable(AtomRadiiTable):
+    """Covalent radii from Cordero et al., 2008, doi:10.1039/b801115j.
+
+    Instantiation of this class requires the periodictable module.
+    """
+
+    # class variable that holds the periodictable.elements object
+    _elements = None
+
+    def _standardLookup(self, smbl):
+        """Return covalent atom radius in Angstroms.
+
+        Attributes
+        ----------
+        smbl
+            string symbol of an element
+
+        Return float.  Raise ValueError for unknown element symbol.
+        """
+        if CovalentRadiiTable._elements is None:
+            from periodictable import elements
+
+            CovalentRadiiTable._elements = elements
+        e = self._elements.isotope(smbl)
+        rv = e.covalent_radius
+        if rv is None:
+            emsg = "Undefined covalent radius for %r." % smbl
+            raise ValueError(emsg)
+        return rv
+
+    # HasClassRegistry overloads:
+
+    def create(self):
+        """Create new instance of the CovalentRadiiTable."""
+        return CovalentRadiiTable()
+
+    def clone(self):
+        """Return a new duplicate instance of self."""
+        import copy
+
+        return copy.copy(self)
+
+    def type(self):
+        """Unique string identifier of the CovalentRadiiTable type.
+
+        This is used for class registration and as an argument for the
+        createByType function.
+
+        Return string.
+        """
+        return "covalent"
+
+
+# End of class CovalentRadiiTable
+CovalentRadiiTable()._registerThisType()
+
+# End of file

diffpy/srreal/attributes.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2010 The Trustees of Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+"""class Attributes  -- wrapper to C++ class diffpy::Attributes
+A base to PairQuantity and quite a few other classes.
+"""
+
+__all__ = ["Attributes"]
+
+from diffpy.srreal.srreal_ext import Attributes
+
+# Inject the __getattr__ and __setattr__ methods to the Attributes class
+
+
+def _getattr(self, name):
+    """Lookup a C++ double attribute if standard Python lookup fails.
+
+    Raise AttributeError if C++ double attribute does not exist.
+    """
+    rv = self._getDoubleAttr(name)
+    return rv
+
+
+Attributes.__getattr__ = _getattr
+
+
+def _setattr(self, name, value):
+    """Assign to C++ double attribute if Python attribute does not
+    exist."""
+    try:
+        object.__getattribute__(self, name)
+    except AttributeError:
+        if self._hasDoubleAttr(name):
+            self._setDoubleAttr(name, value)
+            return
+    object.__setattr__(self, name, value)
+    return
+
+
+Attributes.__setattr__ = _setattr
+
+# Helper accessor functions used by the _registerDoubleAttribute method
+
+
+def _pyattrgetter(name):
+    def f(obj):
+        return object.__getattribute__(obj, name)
+
+    return f
+
+
+def _pyattrsetter(name):
+    def f(obj, value):
+        object.__setattr__(obj, name, value)
+
+    return f
+
+
+# End of file

diffpy/srreal/bondcalculator.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.srreal     by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2011 The Trustees of Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+"""Class BondCalculator -- distances between atoms in the structure."""
+
+# exported items, these also makes them show in pydoc.
+__all__ = ["BondCalculator"]
+
+from diffpy.srreal import srreal_ext as _srreal_ext
+from diffpy.srreal.srreal_ext import BondCalculator as _BondCalculator
+from diffpy.srreal.wraputils import (
+    propertyFromExtDoubleAttr,
+    setattrFromKeywordArguments,
+)
+
+
+class BondCalculator(_BondCalculator):
+    __doc__ = _BondCalculator.__doc__
+
+    def __init__(self, **kwargs):
+        """Create a new instance of BondCalculator. Keyword arguments can be
+        used to configure calculator properties, for example:
+
+        bdc = BondCalculator(rmin=1.5, rmax=2.5)
+
+        Raise ValueError for invalid keyword argument.
+        """
+        super().__init__()
+        setattrFromKeywordArguments(self, **kwargs)
+        return
+
+    def __call__(self, structure=None, **kwargs):
+        """Return sorted bond distances in the specified structure.
+
+        Attributes
+        ----------
+        structure
+            structure to be evaluated, an instance of diffpy Structure
+            or pyobjcryst Crystal.  Reuse the last structure when None.
+        kwargs
+            optional parameter settings for this calculator
+
+        Return a sorted numpy array.
+        """
+        setattrFromKeywordArguments(self, **kwargs)
+        self.eval(structure)
+        return self.distances
+
+
+# property wrappers to C++ double attributes
+
+BondCalculator.rmin = propertyFromExtDoubleAttr(
+    "rmin",
+    "Lower bound for the bond distances. [0 A]",
+)
+
+BondCalculator.rmax = propertyFromExtDoubleAttr(
+    "rmax",
+    "Upper bound for the bond distances. [5 A]",
+)
+
+
+# Historical pickles and direct extension imports use this public name.
+_srreal_ext.BondCalculator = BondCalculator
+
+# End of file